I think that occasions where there is an audience, such as festivals and others, the disobedient pokemon should be desqualified. It will ruin everyone's show since people went to see a great battle, and also because, since the trainer has lost control, the pokemon is incapable of battling, and in my oppinion should receive an immediate defeat. In other cases such as gym battles (even though my second point still stands) I don't think there should be desqualifications, since they are looking for the strongest pokemon, and a disobedient pokemon can be strong (as an example we have Ash's Charizard) and they have no need to look "nice" (since there is no audience).